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Time And Temperature Stability Of Tritrichomonas Foetus In Phosphate-Buffered Saline As Evaluated By A Reverse Transcription Real-Time Pcr Assay And Field Analysis, Duan S. Loy, Renata Spuri Gomes, Enakshy Dutta, Bruce W. Brodersen, John Dustin Loy

School of Veterinary and Biomedical Sciences: Faculty Publications

Tritrichomonas foetus (TF) is a significant reproductive pathogen of cattle, and sample collection, handling, transport, and testing are significant hurdles to surveillance programs. Recent methods have been developed that allow for the direct detection of TF using a reverse transcription real-time PCR (direct RT-qPCR) approach. To evaluate these methods, a comparative analysis was conducted to assess the technical performance of this assay with a commercially available real- time PCR (qPCR) assay. In addition, the evaluation of two types of collection media (PBS and TF transport tube) was conducted that evaluated sample stability from 0 to 3 days when stored at …

Integrating And Optimizing Genomic, Weather, And Secondary Trait Data For Multiclass Classification, Vamsi Manthena, Diego Jarquín, Reka Howard

Department of Statistics: Faculty Publications

Modern plant breeding programs collect several data types such as weather, images, and secondary or associated traits besides the main trait (e.g., grain yield). Genomic data is high-dimensional and often over-crowds smaller data types when naively combined to explain the response variable. There is a need to develop methods able to effectively combine different data types of differing sizes to improve predictions. Additionally, in the face of changing climate conditions, there is a need to develop methods able to effectively combine weather information with genotype data to predict the performance of lines better. In this work, we develop a novel …

Mechanism Of Sphingolipid Homeostasis Revealed By Structural Analysis Of Arabidopsis Spt-Orm1 Complex, Peng Liu, Tian Xie, Xinyue Wu, Gongshe Han, Sita D. Gupta, Zike Zhang, Jian Yue, Feitong Dong, Kenneth Gable, Somashekarappa Niranjanakumari, Wanyuan Li, Lin Wang, Wenchen Liu, Ruifeng Yao, Edgar B. Cahoon, Teresa M. Dunn, Xin Gong

Center for Plant Science Innovation: Faculty Publications

The serine palmitoyltransferase (SPT) complex catalyzes the first and rate-limiting step in sphingolipid biosynthesis in all eukaryotes. ORM/ORMDL proteins are negative regulators of SPT that respond to cellular sphingolipid levels. However, the molecular basis underlying ORM/ORMDL-dependent homeostatic regulation of SPT is not well understood.We determined the cryo–electron microscopy structure of Arabidopsis SPT-ORM1 complex, composed of LCB1, LCB2a, SPTssa, and ORM1, in an inhibited state. A ceramide molecule is sandwiched between ORM1 and LCB2a in the cytosolic membrane leaflet. Ceramide binding is critical for the ORM1-dependent SPT repression, and dihydroceramides and phytoceramides differentially affect this repression. A hybrid β sheet, formed …

Artificial Neural Network-Based Prediction Assessment Of Wire Electric Discharge Machining Parameters For Smart Manufacturing, Itagi Vijayakumar Manoj, Sannayellappa Narendranath, Peter Madindwa Mashinini, Hargovind Soni, Shanay Rab, Shadab Ahmad, Ahatsham Hayat

Department of Electrical and Computer Engineering: Faculty Publications

Artificial intelligence (AI), robotics, cybersecurity, the Industrial Internet of Things, and blockchain are some of the technologies and solutions that are combined to produce “smart manufacturing,” which is used to optimize manufacturing processes by creating and/or accepting data. In manufacturing, spark erosion technique such as wire electric discharge machining (WEDM) is a process that machines different hard-to-cut alloys. It is regarded as the solution for cutting intricate parts and materials that are resistant to conventional machining techniques or are required by design. In the present study, holes of different radii, i.e. 1, 3, and 5mm, have been cut on Nickelvac-HX. …

Diverse Portfolios: Investing In Tributaries For Restoration Of Large River Fishes In The Anthropocene, Kristen L. Bouska, Brian D. Healy, Michael J. Moore, Corey G. Dunn, Jonathan J. Spurgeon, Craig P. Paukert

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Rehabilitation of large Anthropocene rivers requires engagement of diverse stakeholders across a broad range of sociopolitical boundaries. Competing objectives often constrain options for ecological restoration of large rivers whereas fewer competing objectives may exist in a subset of tributaries. Further, tributaries contribute toward building a “portfolio” of river ecosystem assets through physical and biological processes that may present opportunities to enhance the resilience of large river fishes. Our goal is to review roles of tributaries in enhancing mainstem large river fish populations. We present case histories from two greatly altered and distinct large-river tributary systems that highlight how tributaries contribute …

A Plea For Scale, And Why It Matters For Invasive Species Management, Biodiversity And Conservation, Nicholas A. Mcmillan, Samuel D. Fuhlendorf, Craig A. Davis, Robert G. Hamilton, Landon. K. Neumann, Samantha M. Cady

Department of Agronomy and Horticulture: Faculty Publications

1. Invasive species are suspected to be major contributors to biodiversity declines worldwide. Counterintuitively, however, invasive species effects are likely scale dependent and are hypothesized to be positively related to biodiversity at large spatial scales. Past studies investigating the effect of invasion on biodiversity have been mostly conducted at small scales (<100 m²) that cannot represent large dynamic landscapes by design. Therefore, replicated experimental evidence supporting a negative effect of invasive plants on biodiversity is lacking across many landscape types, including large grasslands.

2. We collected data across eight large (333–809 ha) grassland landscapes managed with pyric herbivory—that is the recoupling …

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Spatial And Temporal Patterns Of Red Foxes And Coyotes Through Camera Traps And Citizen Science, Nadia Wojcik

Honors Program: Senior Projects (Public)

Wildlife may change their temporal activity patterns or spatial distribution in response to human activity in developed landscapes. Citizen science and camera trap approaches have both been used to study wildlife in urban areas, though both methods have their strengths and weaknesses. I studied the temporal activity and spatial occurrence of red foxes (Vulpes vulpes) and coyotes (Canis latrans) in Lincoln, Nebraska to test ecological and methodological hypotheses. Specifically, I compared camera trap detections of red foxes and coyotes to observations of red foxes made by residents of Lincoln. Using these two data streams, I evaluated temporal activity patterns and …

A Push–Pull Strategy To Suppress Stable Fly (Diptera: Muscidae) Attacks On Pasture Cattle Via A Coconut Oil Fatty Acid Repellent Formulation And Traps With M-Cresol Lures, Alexander T. Lehmann, Gary J. Brewer, David J. Boxler, Junwei J. Zhu, Kathy Hanford, David Taylor, James A. Kenar, Steven C. Cermak, Jerome A. Hogsette

Department of Entomology: Faculty Publications

BACKGROUND: Stable flies [Stomoxys calcitrans (L.)] are economically important pests of cattle and other livestock. As an alternative to conventional insecticides, we tested a push–pull management strategy using a coconut oil fatty acid repellent formulation and an attractant-added stable fly trap.

RESULTS: In our field trials we found that weekly applications of a push–pull strategy can reduce stable fly populations on cattle as well as a standard insecticide (permethrin). We also found that the efficacy periods of the push–pull and permethrin treatments following on-animal application were equivalent. Traps with an attractant lure used as the pull component of the …

Pen Surface Temperature As A Predictor Of Dailywater Intake And Tympanic Temperature In Steers Finished In Feedlots, Rodrigo A. Arias, Terry L. Mader

Department of Animal Science: Faculty Publications

Adequate estimation of water demand in cattle production feed yards is of high importance, especially due to reduced water availability because of changes in rain precipitation patterns and amounts. The pen surface in feed yards receives and reflects solar radiation, affecting along with other factors the microclimate to which cattle are exposed. This study aimed to describe the relationship between the pen surface temperature with the daily water intake and the tympanic temperature of finishing steers. Climate variables, including solar radiation, air temperature, relative humidity, and wind speed plus pen surface temperature and soil temperature at 10.2 cm depth were …

Evaluation Of Four Thermal Comfort Indices And Their Relationship With Physiological Variables In Feedlot Cattle, Rodrigo A. Arias, Terry L. Mader

Department of Animal Science: Faculty Publications

Climatic data from different years and experiments conducted in Nebraska were used to estimate four comfort thermal indices and to predict the risk of heat stress and its relationship with pen surface temperature (PST). These included the temperature–humidity index (THI), the adjusted THI (THI_adj), the heat load index (HLI), and THI_PST using pen surface temperature instead of air temperature. Respiration rates (RR), tympanic temperatures (TT), and panting scores (PS) were also collected in each year and from each location. During 2007, mean values of soil temperature, PST, outgoing shortwave radiation, and TT were greater than in 2008 …

Differentiating Between Urban Flood Risk As A Unitary Problem And As A Strand In A Braided Problem Set: Implications For Administrative Coordination, Sarah Michaels

Department of Political Science: Faculty Publications

Flood protection is a leading priority for urban water sustainability. Making cities more resilient to flooding has become urgent as the climate changes and as cities increasingly become the loci of human population and resources. Reducing the risk of future flooding in cities often necessitates different jurisdictions working together. They may do so because they confront a shared problem. This was the case in the City of Lincoln, Nebraska, USA, when partnering agencies shared a single focus on reducing flood risk from Beal Slough to the Nebraska State Penitentiary. In contrast, entities may band together to confront braided problems, intertwined …

Invertebrate Metrics Based On Few Abundant Taxa Outperform Functional And Taxonomic Composition As Indicators Of Agricultural Impacts In Atlantic Rainforest Streams, Rafael Feijó‑Lima, Steven A. Thomas, Flavia Tromboni, Eugenia Zandonà, Eduardo F. Silva‑Junior, Timothy P. Moulton

School of Natural Resources: Faculty Publications

Metacommunity studies have demonstrated that local macroinvertebrate communities are structured not only by local environmental conditions but also by spatial processes. Effective bioassessment tools should account for spatial processes while doing so with the least amount of cost. In this study, we applied variance partition techniques based on redundancy analysis to assess the performance of three sets of benthic invertebrate metrics in detecting agricultural land-use effects in a SE Brazil rainforest watershed. Macroinvertebrate data were analyzed separately regarding their taxonomic, functional structure and bioindicator metrics developed for the study region. We stipulated that groups of metrics most sensitive to land-use …

Small Rnas >26 Nt In Length Associate With Ago1 And Are Upregulated By Nutrient Deprivation In The Alga Chlamydomonas, Yingshan Li, Eun-Jeong Kim, Adam Voshall, Etsuko Moriyama, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, …

Efficient Two-Stage Analysis For Complex Trait Association With Arbitrary Depth Sequencing Data, Zheng Xu, Song Yan, Shuai Yuan, Cong Wu, Sixia Chen, Zifang Guo

School of Computing: Faculty Publications

Sequencing-based genetic association analysis is typically performed by first generating genotype calls from sequence data and then performing association tests on the called genotypes. Standard approaches require accurate genotype calling (GC), which can be achieved either with high sequencing depth (typically available in a small number of individuals) or via computationally intensive multi-sample linkage disequilibrium (LD)-aware methods. We propose a computationally efficient two-stage combination approach for association analysis, in which single-nucleotide polymorphisms (SNPs) are screened in the first stage via a rapid maximum likelihood (ML)-based method on sequence data directly (without first calling genotypes), and then the selected SNPs are …

Evaluation Of Peroxyacetic Acid, Liquid Buffered Vinegar, And Cultured Dextrose Fermentate As Potential Antimicrobial Interventions For Raw Chicken Livers, Leslie Pearl M. Cancio, Mary-Grace C. Danao, Gary Sullivan, Byron D. Chaves

Department of Nutrition and Health Sciences: Faculty Publications

This study aimed to evaluate the use of peroxyacetic acid (PAA), buffered vinegar (BV), and cultured dextrose fermentate (CDF) to reduce Salmonella on artificially inoculated raw chicken livers, one of the most consumed offal around the world. Samples were inoculated with a 5-strain cocktail of poultry-borne Salmonella to obtain 10⁶ CFU/g and immersed for 90 s with agitation in one of the following treatments: distilled water (control), 450 ppm PAA, 2.0% (w/v) BV, or 1.5% (w/v) CDF, prior to storing at 4^oC. Salmonella was enumerated on XLD agar and monitored for 14 days. Data were analyzed using …

Atlas Of Ticks (Acari: Argasidae, Ixodidae) In Germany: 1st Data Update, Franz Rubel, Stefan Zaenker, Alexander Weigand, Dieter Weber, Lidia Chitimia-Dobler, Olaf Kahl

Harold W. Manter Laboratory of Parasitology: Library Materials

The first data update of the atlas of ticks in Germany published in 2021 is presented here. This atlas provides maps based on georeferenced tick locations of 21 species endemic in Germany as well as three tick species that are regularly imported to Germany. The data update includes the following numbers of newly georeferenced tick locations: 17 Argas reflexus, 79 Carios vespertilionis, 2 Dermacentor marginatus, 43 Dermacentor reticulatus, 4 Haemaphysalis concinna, 3 Haemaphysalis punctata, 3 Hyalomma rufipes, 3 Ixodes apronophorus, 9 Ixodes arboricola, 1 Ixodes ariadnae, 30 Ixodes canisuga, …

Nebraska Farmland Values And Cash Rental Rates In 2023, Jim Jansen, Jeffrey Stokes

Cornhusker Economics

The market value of agricultural land in Nebraska increased by 14% over the prior year to an average of US $3,835 per acre, according to the 2023 Nebraska Farm Real Estate Market Survey. This marks the second-largest increase in the market value of agricultural land in Nebraska since 2014 and the highest non-inflation-adjusted state-wide land value in the 45-year history of the survey.

The University of Nebraska-Lincoln’s Department of Agricultural Economics annually surveys land industry professionals across Nebraska, including appraisers, farm and ranch managers, agricultural bankers, and related industry professionals. Results from the survey are divided by land class and …

Fresh Produce As A Potential Vector And Reservoir For Human Bacterial Pathogens: Revealing The Ambiguity Of Interaction And Transmission, Ahmed Esmael, Rashad R. Al-Hindi, Raed S. Albiheyri, Mona G. Alharbi, Amani A. R. Filimban, Mazen S. Alseghayer, Abdulaziz M. Almaneea, Meshari Ahmed Alhadlaq, Jumaa Ayubu, Addisu D. Teklemariam

Nebraska Center for Virology: Faculty Publications

The consumer demand for fresh produce (vegetables and fruits) has considerably increased since the 1980s for more nutritious foods and healthier life practices, particularly in developed countries. Currently, several foodborne outbreaks have been linked to fresh produce. The global rise in fresh produce associated with human infections may be due to the use of wastewater or any contaminated water for the cultivation of fruits and vegetables, the firm attachment of the foodborne pathogens on the plant surface, and the internalization of these agents deep inside the tissue of the plant, poor disinfection practices and human consumption of raw fresh produce. …

Spoilage Pseudomonas Survive Common Thermal Processing Schedules And Grow In Emulsified Meat During Extended Vacuum Storage, Samuel C. Watson, Rebecca A. Furbeck, Samodha C. Fernando, Byron D. Chaves, Gary Sullivan

Department of Animal Science: Faculty Publications

Some Pseudomonas species are common meat spoilage bacteria that are often associated with the spoilage of fresh meat. The recently reported ability of these bacteria to also spoil cooked and vacuum packaged meat products has created the need to investigate all potential routes of spoilage they may be able to utilize. The objective of this experiment was to determine if spoilage Pseudomonas spp. survive thermal processing and grow during refrigerated storage under vacuum. Pseudomonas spp. isolates collected from spoiled turkey products were inoculated into a salted and seasoned meat emulsion that was vacuum sealed and thermally treated to final temperatures …

Large And Stable Genome Edits At The Sorghum Alpha Kafirin Locus Result In Changes In Chromatin Accessibility And Globally Increased Expression Of Genes Encoding Lysine Enrichment, J. Preston Hurst, Abou Yobi, Aixia Li, Shirley Sato, Thomas E. Clemente, Ruthie Angelovici

Department of Agronomy and Horticulture: Faculty Publications

Introduction: Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it’s grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus.

Methods: A single consensus …

Drought Affects Sex Ratio And Growth Of Painted Turtles In A Long-Term Study In Nebraska, Larkin A. Powell, Ellen P. Dolph, Charrissa R. Neil

School of Natural Resources: Faculty Publications

Climate forecasts suggest the Great Plains of North America have increased risk of droughts during global warming. Environmental factors have potential to influence turtle populations in aquatic habitats through temperature-dependent sex determination and influences on food availability. Long-term studies are critical to evaluate the influence of climatic variation on turtles. We used a 12-year set of mark-recapture data collected from painted turtles (Chrysemys picta, n = 162) in a pond in Keith County, Nebraska during 2005–2016 to assess variation in sex ratio and growth dynamics. Southwest Nebraska experienced two periods of drought during our study (Palmer Hydrologic Drought …

Plant Breeding Advancements With “Crispr-Cas” Genome Editing Technologies Will Assist Future Food Security, M. Ahmad

Center for Plant Science Innovation: Faculty Publications

Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world’s population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic …

Nebraska Politics And The Environment: Framing Political Communication In The State Of Nebraska In Comparison To National Level Discourse, Samuel Taylor

Honors Program: Senior Projects (Public)

Environmental public policy has seen little change on the national level in recent decades due to Congressional gridlock. Politicians on both sides of the aisle have entrenched their opposing viewpoints, and their communication on the topic utilizes issue frames to help sway the public to see their side. On the Republican side, these issue frames take the form of the “scientific uncertainty” and “economic consequences” frames. This study, based on issue framing, surveys the communication of Nebraska’s Republican State Senators to determine if they utilize the same issue frames or if they diverge from their national counterparts. By analyzing recent …

Divination, Brannon Evans

Honors Program: Senior Projects (Public)

This document details my time developing a cross-discipline devised theatre experience. The piece explores the various ways we interact with technology. The start of the process was fueled by one simple question: “What can multi faceted collaboration look like (between peers– not just across disciplines, but through an equally shared devising process)?” Through this documentation, I will be able to reflect upon and learn from my experience as a facilitator, actor, and theatre maker.

This thesis will be broken into six different parts to outline the six stages I underwent while creating the piece: developing the team, source material exploration, …

Association Of Excessive Precipitation And Agricultural Land Use With Honey Bee Colony Performance, Gabriela M. Quinlan, Rufus Isaacs, Clint R. V. Otto, Autumn H. Smart, Meghan O. Milbrath

Department of Entomology: Faculty Publications

Context From landscape variables to weather, multiple environmental factors affect honey bees and other pollinators. Detailed honey bee colony assessments in a variety of landscape and weather conditions offer the opportunity to develop a mechanistic understanding of how landscape composition, configuration, and weather are associated with colony nutrition, demography, and productivity.

Objectives Our objective was to test if weather and landscape characteristics (e.g., agricultural versus forested land use) are associated with different honey bee colony outcomes (foraged nectar mass, foraged pollen mass, pupal population size, and adult population size change).

Methods We collected detailed colony measurements on over 450 honey …

Evidence For A Causal Role For Escherichia Coli Strains Identified As Adherent-Invasive (Aiec) In Intestinal Inflammation, Hatem Kittana, Joao Carlos Gomes-Neto, Kari Heck, Anthony Juritsch, Jason Sughroue, Yibo Xian, Sara Mantz, Rafael R. Segura Muñoz, Liz Cody, Robert J. Schmaltz, Christopher L. Anderson, Rodney A. Moxley, Jesse M. Hostetter, Samodha C. Fernando, Jennifer Clarke, Stephen D. Kachman, Clayton E. Cressler, Andrew K. Benson, Jens Walter

Department of Nutrition and Health Sciences: Faculty Publications

Enrichment of adherent-invasive Escherichia coli (AIEC) has been consistently detected in subsets of inflammatory bowel disease (IBD) patients. Although some AIEC strains cause colitis in animal models, these studies did not systematically compare AIEC with non-AIEC strains, and causal links between AIEC and disease are still disputed. Specifically, it remains unclear whether AIEC shows enhanced pathogenicity compared to that of commensal E. coli found in the same ecological microhabitat and if the in vitro phenotypes used to classify strains as AIEC are pathologically relevant. Here, we utilized in vitro phenotyping and a murine model of intestinal inflammation to systematically compare …

2023 Ag Law Legislative Update, J. David Aiken

Cornhusker Economics

Covers agricultural law legislation in the Nebraska Unicameral in 2023, including LB 401 (Nebraska mesonet system funding), LB 591 (farmland leases), and LB 662 (livestock nuisance lawsuits).

Advertising Sports Nutrition Practices To Adolescent Athletes: A Poster Series, Emma Hansen

Honors Program: Senior Projects (Public)

Sports nutrition is an important aspect of an athlete’s training and improvement, yet it is often overlooked when it comes to younger competitors. Four posters were created with the intent of providing adolescent athletes, their parents, and their coaches with information about important topics in sports nutrition including a general overview of nutrition goals, hydration strategies, recovery nutrition, and nutritional considerations for vegetarian and vegan youth athletes. The posters were designed to appeal to adolescents from the ages of 13 to 18, and each poster covers its designated topic in detail appropriate for middle and high school-aged athletes. The accompanying …

The Center For Agricultural Profitability Contributes To Collaborative Adaptive Management Project At The Barta Brothers Ranch, Jay Parsons, Mitchell B. Stephenson, Kyle Martens

Cornhusker Economics

In 2020, the University of Nebraska's Barta Brothers Ranch (BBR) launched a collaborative adaptive management (CAM) project to address risks and uncertainties related to grassland management in the Sandhills. The project brings together UNL faculty engaged in research, extension and teaching across multiple disciples, departments and geographic locations. All three Institute of Agriculture and Natural Resources (IANR) District Research, Extension, and Education Centers are involved the project (Eastern Nebraska, Panhandle, and West Central) along with three East Campus based centers: the Center for Grassland Studies, the Center for Resilience in Agricultural Working Landscapes, and the Center for Agricultural Profitability housed …

Functional Annotation Of The Animal Genomes: An Integrated Annotation Resource For The Horse, Sichong Peng, Anna R. Dahlgren, Callum G. Donnelly, Erin N. Hales, Jessica Lynn Petersen, Rebecca R. Bellone, Ted Kalbfleisch, Carrie J. Finno

Department of Animal Science: Faculty Publications

The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNAseq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To …